Dataset Information


Arabidopsis thaliana small RNAs sequences identified using high-throughput 454 sequencing technology

ABSTRACT: To determine the extent to which the major small RNA pathways functions across the Arabidopsis thaliana genome, small RNA populations from several tissues of wild-type (wt) and mutant plants were amplified by RT-PCR and sequenced using high-throughput 454 sequencing technology. Keywords: small RNAs, high-throughput sequencing Amplicons were prepared by 5' and 3' adaptor ligation and RT-PCR using small RNA fractions from inflorescence tissue (containing stage 1-12 flowers) of wt Col-0 plants, mutants with defects in each DCL gene (dcl1-7, dcl2-1, dcl3-1, dcl4-2), and mutants with defects in each RDR gene for which a function has been established (rdr1-1, rdr2-1, rdr6-15). Amplicons from whole seedlings (3 day post-germinations) were prepared from Col-0 and rdr6-15 plants. Small RNA preparations from leaf samples of Col-O that were either uninoculated or inoculated by Pseudomonas syringae pv tomato (DC3000hrcC) for 1 hr and 3 hr were also sequenced.

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: James C Carrington   Jason S Cumbie  Kristin D Kasschau  Christopher M Sullivan  Elisabeth J Chapman  Noah Fahlgren 

PROVIDER: E-GEOD-6682 | ArrayExpress | 2007-02-01



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Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting.

Howell Miya D MD   Fahlgren Noah N   Chapman Elisabeth J EJ   Cumbie Jason S JS   Sullivan Christopher M CM   Givan Scott A SA   Kasschau Kristin D KD   Carrington James C JC  

The Plant cell 20070330 3

Posttranscriptional RNA silencing of many endogenous transcripts, viruses, and transgenes involves the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 (RDR6/DCL4)-dependent short interfering RNA (siRNA) biogenesis pathway. Arabidopsis thaliana contains several families of trans-acting siRNAs (tasiRNAs) that form in 21-nucleotide phased arrays through the RDR6/DCL4-dependent pathway and that negatively regulate target transcripts. Using deep sequencing technology and computational approaches, the phasi  ...[more]

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